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Report generated at 2020-07-15 00:27:24

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	82656376	153209202
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	75157017	149479079
Mapped(QC-failed)	0	0
% Mapped	90.9300	97.5700
Paired	82656376	153209202
Paired(QC-failed)	0	0
Read1	41328188	76604601
Read1(QC-failed)	0	0
Read2	41328188	76604601
Read2(QC-failed)	0	0
Properly Paired	74017603	147025154
Properly Paired(QC-failed)	0	0
% Properly Paired	89.5500	95.9600
With itself	74582132	148752334
With itself(QC-failed)	0	0
Singletons	574885	726745
Singletons(QC-failed)	0	0
% Singleton	0.7000	0.4700
Diff. Chroms	252262	985904
Diff. Chroms (QC-failed)	0	0

Marking duplicates (filtered BAM)

Filtered out (samtools view -F 1804):

read unmapped (0x4)
mate unmapped (0x8)
not primary alignment (0x100)
read fails platform/vendor quality checks (0x200)
read is PCR or optical duplicate (0x400)

	rep1	ctl1
Unpaired Reads	0	0
Paired Reads	32022454	64022479
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	81466	238123
Paired Opt. Dupes	1328	1074
% Dupes/100	0.0025	0.0037

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	32016768	63951647
Distinct Read Pairs	31935316	63714783
One Read Pair	31854136	63480345
Two Read Pairs	80915	232360
NRF = Distinct/Total	0.9975	0.9963
PBC1 = OnePair/Distinct	0.9975	0.9963
PBC2 = OnePair/TwoPair	393.6741	273.1982

Mitochondrial reads are filtered out.

NRF (non redundant fraction)
PBC1 (PCR Bottleneck coefficient 1)
PBC2 (PCR Bottleneck coefficient 2)
PBC1 is the primary measure. Provisionally

0-0.5 is severe bottlenecking
0.5-0.8 is moderate bottlenecking
0.8-0.9 is mild bottlenecking
0.9-1.0 is no bottlenecking

Flagstat (filtered/deduped BAM)

Filtered and duplicates removed

	rep1	ctl1
Total	63881976	127568712
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	63881976	127568712
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	63881976	127568712
Paired(QC-failed)	0	0
Read1	31940988	63784356
Read1(QC-failed)	0	0
Read2	31940988	63784356
Read2(QC-failed)	0	0
Properly Paired	63881976	127568712
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	63881976	127568712
With itself(QC-failed)	0	0
Singletons	0	0
Singletons(QC-failed)	0	0
% Singleton	0.0000	0.0000
Diff. Chroms	0	0
Diff. Chroms (QC-failed)	0	0

Peak calling

Reproducibility QC and peak detection statistics

The number of peaks is capped at 300K for peak-caller MACS2

	overlap
Nt	0
N1	88800
Np	0
N optimal	88800
N conservative	88800
Optimal Set	rep1-pr
Conservative Set	rep1-pr
Rescue Ratio	0.0000
Self Consistency Ratio	1.0000
Reproducibility	pass

Overlapping peaks

N1: Replicate 1 self-consistent overlapping peaks (comparing two pseudoreplicates generated by subsampling Rep1 reads)
N2: Replicate 2 self-consistent overlapping peaks (comparing two pseudoreplicates generated by subsampling Rep2 reads)
Nt: True Replicate consisten overlapping peaks (comparing true replicates Rep1 vs Rep2 )
Np: Pooled-pseudoreplicate consistent overlapping peaks (comparing two pseudoreplicates generated by subsampling pooled reads from Rep1 and Rep2 )
Self-consistency Ratio: max(N1,N2) / min (N1,N2)
Rescue Ratio: max(Np,Nt) / min (Np,Nt)
Reproducibility Test: If Self-consistency Ratio >2 AND Rescue Ratio > 2, then 'Fail' else 'Pass'

Enrichment

Strand cross-correlation measures

Performed on subsampled reads (15M)

	rep1
Reads	15000000
Est. Fragment Len.	120
Corr. Est. Fragment Len.	0.1837
Phantom Peak	50
Corr. Phantom Peak	0.2036
Argmin. Corr.	1500
Min. Corr.	0.1762
NSC	1.0425
RSC	0.2731

NOTE1: For SE datasets, reads from replicates are randomly subsampled.
NOTE2: For PE datasets, the first end of each read-pair is selected and the reads are then randomly subsampled.

Normalized strand cross-correlation coefficient (NSC) = col9 in outFile
Relative strand cross-correlation coefficient (RSC) = col10 in outFile
Estimated fragment length = col3 in outFile, take the top value

Fraction of reads in overlapping peaks

	rep1-pr
Fraction of Reads in Peak	0.0789

ppr: Overlapping peaks comparing pooled pseudo replicates
rep1-pr: Overlapping peaks comparing pseudoreplicates from replicate 1
rep2-pr: Overlapping peaks comparing pseudoreplicates from replicate 2
repi-repj: Overlapping peaks comparing true replicates (rep i vs. rep j)

Other quality metrics

Fingerprint and Jensen-Shannon distance

	rep1
% genome enriched	0.2705
AUC	0.4949
CHANCE divergence	0.1120
Elbow Point	0.0000
JS Distance	0.5960
Synthetic AUC	0.4961
Synthetic Elbow Point	0.1190
Synthetic JS Distance	0.2884